On 1 Jun 2006, at 05:58, Pallavi Sarmah wrote:
Hi
Hi Pallavi,
I ve sent a mail on 30 th may. Since I have received no reply and also
it didn't appear in the mail archive I m afraid it must have nt been
delivered. I m forwarding the mail again.
Waiting for a suggestion.
this is because you sent your email directly to me rather than to
mart-dev :-)
It is always safer to send an email to the list because there are more
people
who could respond quickly.
The problem you describe is best tested by writing a simple java class
which connects to the database just to check if this some sort of JDBC/
db privileges problem or rather a BioMart problem (obviously run from
the
same machine and with the same connection string). Could you check
that and tell us if you are able to do it without BioMart code? We'll
then
look into this in more detail
cheers,
a.
Thank you
Regards,
Pallavi
-----Original Message-----
From: Pallavi Sarmah
Sent: Tuesday, May 30, 2006 12:07 PM
To: 'Arek Kasprzyk'
Subject: RE: [mart-dev] cannot connect to local database.
Hi
I am trying to install biomart locally in my machine. Bt I m nt being
able to connect martj to a database. I ve msd_mart_4 table structures
(without data) locally. I ve modified the defaultmartregistry file both
in martj n biomart-plib. But still I m nt being able to connect and the
error msg that I get is as follows
Include a correct meta_version_version__main table
entry:java.sql.SQLException:Invalid authorization specification message
from server: "Access denied for user
'root'@'localhost.localdomain'(using password:YES)"
While root do have access to the database. I ve tried with other users
bt still I get the same msg. I am also sending u the
defaultmartregistry
file for yr reference.
<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE MartRegistry (View Source for full doctype...)>
- <MartRegistry>
<MartDBLocation name="Local BioMart"
displayName="Local BioMart Database"
databaseType="mysql"
host="localhost"
port="3306"
database="msd_mart_4"
schema="msd_mart_4"
includeDatasets=""
user="root"
password="pallu"
visible="1"
default=""
martUser=""
/>
</MartRegistry>
Regards,
Pallavi
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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